Molecular characterization of Major Viral Hepatotrophs Co-infected with HIV from sera collected in the North West and Kwa-Zulu Natal Provinces of South Africa

Abstract

Blood borne infections by HBV, HCV and HIV represent a major public health problem globally. The co-infection of HIV with HBV/ HCV is globally common owing to shared route of bloodborne transmission. From 36 million people infected with HIV, close to 4 million people were reported to be infected with HBV and 5 million were infected with HCV (WHO, 2017). These two major hepatotrophs increase the HIV pathogenesis and have emerged as a major cause of death in HIV-infected patients. In South Africa HIV/HBV co-infections substantially out-number HIV/HCV co-infections; close to 63% South Africans living with HIV have been exposed to HBV with chronic HBV ranging from 5-20% in various studies of HIV-infected individuals (Scheibe, 2017). But in South Africa the HCV prevalence is reported to range from 0.16 to 1.8% (Hecht et al., 2018). HCV co-infection is less common, reflecting the magnitude of injecting drug use. Currently, the prevalence of HIV-infected individuals co-infected with both HBV/ HCV is uncertain. There is still limited data on the HBV/ HCV genotypes circulating in HIV-infected individuals in the North West Province and KwaZulu-Natal, these two provinces have the highest number of people infected with HIV suggesting that co-infection with HBV and HCV might be present. Co-infection of HBV and HCV in HIV infected people may hinder treatment and management of these viruses in the context of co-infections and result in progressive HIV replication and death in HIV-infected patients. The aim of this study was to determine the molecular prevalence of HBV and HCV in HIV-infected individuals from Durban, KwaZulu-Natal and pregnant women from Mahikeng, North West Province. Using serology and genotyping methods we identified the prevalence of HBV/ HCV in HIV infected individuals and we characterized HIV, HBV and HCV genetic types in co-infected individuals. Co-infected individuals were further characterized for mutations associated with drug resistance. HBV/ HIV co-infection from Mahikeng cohort was 9% (2/23) based on Polymerase chain reaction amplification of the HBV partial surface gene. From the Durban cohort, HBV/HIV co-infection was 78% (41/50) based on PCR amplification of the HBV partial surface and 10% (5/50) for amplification of the BCP/PC gene. There was no HBV/HCV and HCV/HIV co-infection identified from both cohorts. Genotyping of HBV and HIV was done through PCR amplification, Sanger sequencing and phylogenetic analysis. Sequence and phylogenetic analysis indicated that all HIV sequences from both cohorts from this study clustered with HIV genotype 1 and HBV sequences belonged to HBV genotype A. Both HBV and HIV genotypes identified in this study are predominant among heterosexual populations in South Africa. The prevalence of mutations on the HIV pol region from Mahikeng cohort was 17% (4/23). HIV pol region contained mutations associated with resistance to NRTIs and NNRTIs drugs such as K103N, M184I, M230L and K65R which according to the Stanford Genotypic Resistance Interpretation Algorithm are considered major mutations, were detected indicating possible transmission of anti-retroviral drug resistance mutations since the cohort was antiretroviral therapy naïve. The prevalence of mutations on the HIV pol region from Durban was 0% (0/50). The prevalence of mutations on the BCP/PC region of HBV from Mahikeng was 0% (0/23) whilst it was 16% (6/38) from Durban cohort. The BCP/PC sequences had mutations; A1762G, T1753C, A1762T, G1764A, C1766T, G1862A and also GCAC Kozak sequence was identified as a variant and may cause immune escape HBV. From the Mahikeng cohort prevalence of mutants on the overlapping HBsAg region of HBV was 25% (1/4) and the prevalence on RT region of the HBV polymerase region was 75% (3/4). Mutant identified on the overlapping HBsAg region of HBV was S207N and on the RT region of the HBV polymerase we identified M129L, V163I and I253Y. S207N mutant is associated with poor HBsAg antigenicity whilst V163I and I253Y mutants on the RT region are associated with resistance to LMV, LdT and ADV. From the Durban cohort, mutations prevalence in the HBsAg region was 47% (18/38). The most common mutation was S207N at 71%, followed by L216V and A194V at 23%, P70H at 21%, L209V at 18%, P217L at 8%, F134L, E164D and T189I at 5%, S204R, S117N, T143S, G145R, Y206H, P127T, Y200T, F129T and K122R all at 3%. From the Durban cohort, the prevalence of mutations associated with drug resistance was 50% (7/14) within the RT region. Drug resistance mutations included LMV resistance at 57% (4/7), LdT at 57% (4/7), 14% (1/7) for ETF and 43% (3/7) for ADV resistance. Mutations causing resistance to LMV and LdT were M204V, L180M, V163I, and S202K; with S202K also being resistance to ETF and ADV resistance mutation were I253Y, I223V and M250I. The drug susceptibility prevalence was 68% (26/38). Multiple drug resistance mutations within a single sample were identified from sample QQ46 containing L180M, M204V, S202K and M250I mutations. All the mutations associated with drug resistance identified in the polymerase (RT) were identified from genotype A sequences. We have identified HBV genotypes in HIV-infected patients and the HBV mutations present in HBV/HIV co-infected individuals.